data_19745 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of a mismatch DNA ; _BMRB_accession_number 19745 _BMRB_flat_file_name bmr19745.str _Entry_type original _Submission_date 2014-01-21 _Accession_date 2014-01-21 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ghosh Anirban . . 2 Kar Rajiv Kumar . 3 Bhunia Anirban . . 4 Chatterjee Subhrangsu . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 212 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-03-03 original author . stop_ _Original_release_date 2014-03-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution NMR structure of mismatch DNA' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ghosh Anirban . . 2 Kar Rajiv Kumar . 3 Chatterjee Subhrangsu . . 4 Bhunia Anirban . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA (28-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (28-MER), 1' $DNA_(28-MER)_1 'DNA (28-MER), 2' $DNA_(28-MER)_2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(28-MER)_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(28-MER)_1 _Molecular_mass 8608.586 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence GCGCATGCTACGCG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DC 5 DA 6 DT 7 DG 8 DC 9 DT 10 DA 11 DC 12 DG 13 DC 14 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(28-MER)_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(28-MER)_2 _Molecular_mass 8608.586 _Mol_thiol_state 'not present' _Details . _Residue_count 14 _Mol_residue_sequence CGCGTACGATGCGC loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DG 5 DT 6 DA 7 DC 8 DG 9 DA 10 DT 11 DG 12 DC 13 DG 14 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_(28-MER)_1 . . . . . . $DNA_(28-MER)_2 . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $DNA_(28-MER)_1 'chemical synthesis' . . . . . $DNA_(28-MER)_2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(28-MER)_1 1 mM 'natural abundance' D2O 90 % 'natural abundance' H2O 10 % 'natural abundance' $DNA_(28-MER)_2 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.2 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0 internal direct . . . 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (28-MER), 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 DG H1' H 6.24 0.003 1 2 1 1 DG H2' H 2.48 0.003 2 3 1 1 DG H2'' H 2.62 0.003 2 4 1 1 DG H3' H 4.86 0.003 1 5 1 1 DG H4' H 4.30 0.003 1 6 1 1 DG H8 H 7.78 0.005 1 7 2 2 DC H1' H 5.8 0.004 1 8 2 2 DC H2' H 2.45 0.004 2 9 2 2 DC H2'' H 3.31 0.004 2 10 2 2 DC H3' H 4.86 0.004 1 11 2 2 DC H4' H 4.18 0.004 1 12 2 2 DC H5 H 5.30 0.002 1 13 2 2 DC H6 H 7.33 0.004 1 14 2 2 DC H41 H 6.60 0.002 2 15 2 2 DC H42 H 8.46 0.003 2 16 3 3 DG H1 H 13.01 0.003 1 17 3 3 DG H1' H 6.02 0.002 1 18 3 3 DG H2' H 2.68 0.002 2 19 3 3 DG H2'' H 2.75 0.002 2 20 3 3 DG H3' H 4.94 0.002 1 21 3 3 DG H4' H 4.31 0.002 1 22 3 3 DG H8 H 7.98 0.004 1 23 4 4 DC H1' H 5.57 0.006 1 24 4 4 DC H2' H 1.98 0.006 2 25 4 4 DC H2'' H 2.20 0.006 2 26 4 4 DC H3' H 4.78 0.006 1 27 4 4 DC H4' H 4.20 0.006 1 28 4 4 DC H5 H 5.38 0.005 1 29 4 4 DC H6 H 7.41 0.003 1 30 4 4 DC H41 H 6.41 0.002 2 31 4 4 DC H42 H 8.28 0.004 2 32 5 5 DA H1' H 6.18 0.003 1 33 5 5 DA H2' H 2.66 0.005 2 34 5 5 DA H2'' H 2.99 0.002 2 35 5 5 DA H3' H 5.01 0.006 1 36 5 5 DA H4' H 4.41 0.005 1 37 5 5 DA H8 H 8.18 0.004 1 38 5 5 DA H62 H 7.70 0.002 2 39 6 6 DT H1' H 5.86 0.005 1 40 6 6 DT H2' H 1.96 0.002 2 41 6 6 DT H2'' H 2.32 0.004 2 42 6 6 DT H3' H 4.72 0.006 1 43 6 6 DT H4' H 4.24 0.008 1 44 6 6 DT H6 H 7.12 0.006 1 45 6 6 DT H71 H 1.34 0.007 1 46 6 6 DT H72 H 1.34 0.007 1 47 6 6 DT H73 H 1.34 0.007 1 48 7 7 DG H1' H 5.70 0.004 1 49 7 7 DG H2' H 2.52 0.002 2 50 7 7 DG H2'' H 2.71 0.004 2 51 7 7 DG H3' H 5.12 0.003 1 52 7 7 DG H4' H 4.31 0.004 1 53 7 7 DG H8 H 7.88 0.006 1 54 8 8 DC H1' H 5.68 0.006 1 55 8 8 DC H2' H 1.84 0.004 2 56 8 8 DC H2'' H 2.30 0.005 2 57 8 8 DC H3' H 4.75 0.004 1 58 8 8 DC H4' H 4.28 0.005 1 59 8 8 DC H5 H 5.38 0.004 1 60 8 8 DC H6 H 7.40 0.007 1 61 9 9 DT H1' H 5.61 0.02 1 62 9 9 DT H2' H 1.84 0.03 2 63 9 9 DT H2'' H 2.92 0.04 2 64 9 9 DT H3' H 5.12 0.05 1 65 9 9 DT H4' H 4.25 0.07 1 66 9 9 DT H6 H 7.38 0.06 1 67 9 9 DT H71 H 1.44 0.07 1 68 9 9 DT H72 H 1.44 0.07 1 69 9 9 DT H73 H 1.44 0.07 1 70 10 10 DA H1' H 6.20 0.003 1 71 10 10 DA H2' H 2.40 0.005 2 72 10 10 DA H2'' H 2.85 0.002 2 73 10 10 DA H3' H 5.04 0.006 1 74 10 10 DA H4' H 4.48 0.005 1 75 10 10 DA H8 H 8.35 0.004 1 76 10 10 DA H62 H 7.56 0.002 1 77 11 11 DC H1' H 5.66 0.006 1 78 11 11 DC H2' H 1.85 0.004 2 79 11 11 DC H2'' H 2.30 0.005 2 80 11 11 DC H3' H 4.75 0.004 1 81 11 11 DC H4' H 4.28 0.005 1 82 11 11 DC H5 H 5.30 0.004 1 83 11 11 DC H6 H 7.32 0.007 1 84 11 11 DC H41 H 6.54 0.004 2 85 11 11 DC H42 H 8.18 0.005 2 86 12 12 DG H1 H 12.93 0.008 1 87 12 12 DG H1' H 5.98 0.004 1 88 12 12 DG H2' H 2.34 0.002 2 89 12 12 DG H2'' H 2.82 0.004 2 90 12 12 DG H3' H 5.20 0.003 1 91 12 12 DG H4' H 4.44 0.004 1 92 12 12 DG H8 H 7.91 0.006 1 93 13 13 DC H1' H 6.18 0.006 1 94 13 13 DC H2' H 1.98 0.004 2 95 13 13 DC H2'' H 2.39 0.005 2 96 13 13 DC H3' H 4.80 0.004 1 97 13 13 DC H4' H 4.46 0.005 1 98 13 13 DC H5 H 5.47 0.004 1 99 13 13 DC H6 H 7.48 0.007 1 100 13 13 DC H41 H 6.56 0.004 2 101 13 13 DC H42 H 8.46 0.005 2 102 14 14 DG H1 H 10.14 0.008 1 103 14 14 DG H1' H 6.05 0.004 1 104 14 14 DG H2' H 2.26 0.002 2 105 14 14 DG H2'' H 2.90 0.004 2 106 14 14 DG H3' H 5.04 0.003 1 107 14 14 DG H4' H 4.20 0.004 1 108 14 14 DG H8 H 7.72 0.006 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (28-MER), 2' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 15 1 DC H1' H 6.18 0.007 1 2 15 1 DC H2' H 1.74 0.001 2 3 15 1 DC H2'' H 2.44 0.003 2 4 15 1 DC H3' H 4.74 0.002 1 5 15 1 DC H4' H 4.14 0.005 1 6 15 1 DC H6 H 7.40 0.004 1 7 16 2 DG H1 H 13.13 0.003 1 8 16 2 DG H1' H 5.82 0.002 1 9 16 2 DG H2' H 2.52 0.002 2 10 16 2 DG H2'' H 2.65 0.002 2 11 16 2 DG H3' H 4.52 0.002 1 12 16 2 DG H4' H 4.40 0.002 1 13 16 2 DG H8 H 7.95 0.004 1 14 17 3 DC H1' H 5.85 0.006 1 15 17 3 DC H2' H 1.94 0.006 2 16 17 3 DC H2'' H 2.15 0.006 2 17 17 3 DC H3' H 4.94 0.006 1 18 17 3 DC H4' H 4.22 0.006 1 19 17 3 DC H5 H 5.40 0.005 1 20 17 3 DC H6 H 7.95 0.003 1 21 17 3 DC H41 H 6.50 0.002 2 22 17 3 DC H42 H 8.34 0.004 2 23 18 4 DG H1 H 12.83 0.003 1 24 18 4 DG H1' H 6.18 0.002 1 25 18 4 DG H2' H 2.54 0.002 2 26 18 4 DG H2'' H 2.69 0.002 2 27 18 4 DG H3' H 5.00 0.002 1 28 18 4 DG H4' H 4.36 0.002 1 29 18 4 DG H8 H 7.95 0.004 1 30 19 5 DT H1' H 5.58 0.02 1 31 19 5 DT H2' H 2.00 0.003 2 32 19 5 DT H2'' H 2.72 0.04 2 33 19 5 DT H3 H 13.61 0.02 1 34 19 5 DT H3' H 5.18 0.05 1 35 19 5 DT H4' H 4.18 0.07 1 36 19 5 DT H6 H 7.31 0.06 1 37 19 5 DT H71 H 1.54 0.07 1 38 19 5 DT H72 H 1.54 0.07 1 39 19 5 DT H73 H 1.54 0.07 1 40 20 6 DA H1' H 6.20 0.003 1 41 20 6 DA H2' H 2.26 0.005 2 42 20 6 DA H2'' H 2.82 0.002 2 43 20 6 DA H3' H 5.31 0.006 1 44 20 6 DA H4' H 4.64 0.005 1 45 20 6 DA H8 H 8.29 0.004 1 46 21 7 DC H1' H 5.90 0.004 1 47 21 7 DC H2' H 2.36 0.002 2 48 21 7 DC H2'' H 3.05 0.004 2 49 21 7 DC H3' H 5.01 0.003 1 50 21 7 DC H4' H 4.32 0.004 1 51 21 7 DC H5 H 5.32 0.008 1 52 21 7 DC H6 H 7.55 0.006 1 53 22 8 DG H1' H 5.78 0.004 1 54 22 8 DG H2' H 2.46 0.004 2 55 22 8 DG H2'' H 2.78 0.004 2 56 22 8 DG H3' H 4.98 0.004 1 57 22 8 DG H4' H 4.31 0.004 1 58 22 8 DG H8 H 7.65 0.004 1 59 23 9 DA H1' H 6.22 0.003 1 60 23 9 DA H2' H 2.76 0.005 2 61 23 9 DA H2'' H 3.00 0.002 2 62 23 9 DA H3' H 5.10 0.006 1 63 23 9 DA H4' H 4.31 0.005 1 64 23 9 DA H8 H 8.28 0.004 1 65 24 10 DT H1' H 6.22 0.02 1 66 24 10 DT H2' H 1.82 0.03 2 67 24 10 DT H2'' H 2.80 0.04 2 68 24 10 DT H3 H 13.45 0.02 1 69 24 10 DT H3' H 5.16 0.05 1 70 24 10 DT H4' H 4.15 0.07 1 71 24 10 DT H6 H 7.17 0.06 1 72 24 10 DT H71 H 1.38 0.07 1 73 24 10 DT H72 H 1.38 0.07 1 74 24 10 DT H73 H 1.38 0.07 1 75 25 11 DG H1 H 12.62 0.008 1 76 25 11 DG H1' H 5.70 0.004 1 77 25 11 DG H2' H 2.48 0.002 2 78 25 11 DG H2'' H 2.85 0.004 2 79 25 11 DG H3' H 5.18 0.003 1 80 25 11 DG H4' H 4.40 0.004 1 81 25 11 DG H8 H 7.88 0.006 1 82 26 12 DC H1' H 5.91 0.004 1 83 26 12 DC H2' H 2.38 0.004 2 84 26 12 DC H2'' H 3.30 0.004 2 85 26 12 DC H3' H 4.86 0.004 1 86 26 12 DC H4' H 4.15 0.004 1 87 26 12 DC H5 H 5.41 0.002 1 88 26 12 DC H6 H 7.31 0.004 1 89 26 12 DC H41 H 6.40 0.002 2 90 26 12 DC H42 H 8.40 0.002 2 91 27 13 DG H1 H 13.08 0.008 1 92 27 13 DG H1' H 5.80 0.004 1 93 27 13 DG H2' H 2.34 0.002 2 94 27 13 DG H2'' H 2.82 0.004 2 95 27 13 DG H3' H 5.36 0.003 1 96 27 13 DG H4' H 4.48 0.004 1 97 27 13 DG H8 H 7.75 0.006 1 98 28 14 DC H1' H 5.71 0.006 1 99 28 14 DC H2' H 1.92 0.004 2 100 28 14 DC H2'' H 2.30 0.005 2 101 28 14 DC H3' H 4.85 0.004 1 102 28 14 DC H4' H 4.26 0.005 1 103 28 14 DC H5 H 5.31 0.004 1 104 28 14 DC H6 H 7.55 0.007 1 stop_ save_